MedicalDataService

System for storing, indexing and visualizing medical data in DICOM format

Diagrams

1. Use case diagram
2. Activity diagram
3. ER diagram
4. Sequence diagram

Backend setup

1. Install python3.12 interpreter
2. Install dependencies with pip install -r requirements.txt
3. Create a database YOUR_DB_NAME for the project, specify the password for this database for your user.
4. Create .env file in root folder of project with following content:

   DB_HOST = 'localhost'
   DB_PORT = '5438'
   DB_NAME = 'YOUR_DB_NAME'
   DB_USER = 'YOUR_USER'
   DB_PASSWORD = 'YOUR_PASSWORD'
   

   Note that DB_PORT indicates the server version of PostgreSQl, for more info on linux you can run pg_lsclusters
5. Go to app folder, run alembic init -t async migration
6. Move alembic.ini file from app folder to root folder of project (mv alembic.ini ..)
7. In file alemvic.ini change row script_location = migration to script_location = app/migration
8. Open file app/migration/env.py, delete all contents from the beginning of the file up to and including line target_metadata = None (row 23) and insert the following content instead

   import asyncio
   from logging.config import fileConfig
   
   from sqlalchemy import pool
   from sqlalchemy.engine import Connection
   from sqlalchemy.ext.asyncio import async_engine_from_config
   
   from alembic import context
   
   import sys
   from os.path import dirname, abspath
   
   sys.path.insert(0, dirname(dirname(abspath(__file__))))
   
   from app.database import DATABASE_URL, Base
   from app.users.models import User
   
   
   # this is the Alembic Config object, which provides
   # access to the values within the .ini file in use.
   config = context.config
   config.set_main_option("sqlalchemy.url", DATABASE_URL)
   
   # Interpret the config file for Python logging.
   # This line sets up loggers basically.
   if config.config_file_name is not None:
       fileConfig(config.config_file_name)
   
   target_metadata = Base.metadata
   
   # add your model's MetaData object here
   # for 'autogenerate' support
   # from myapp import mymodel
   # target_metadata = mymodel.Base.metadata

   Pay attention to from app.users.models import User, for each table in the database you need to add the corresponding import to this (env.py) file, however, at the moment there is a description only for the users table in app/users
9. Go to root folder of project, run alembic revision --autogenerate -m "Initial revision",
10. Run alembic upgrade head, a users table has now been created in your database. To roll back changes run alembic downgrade -1. For upgrade alternatively you can run alembic upgrade VERSION_ID, where VERSION_ID is id from generated file from folder app/migration/versions which contains a line like Revision ID: VERSION_ID
11. Create certs directory and enter it mkdir certs && cd certs
12. Create RSA256 private certificate openssl genrsa -out jwt-private.pem 2048
13. Create RSA256 public certificate based on private openssl rsa -in jwt-private.pem -outform PEM -pubout -out jwt-public.pem

Usage

Run fastapi dev app/main.py from root folder of project

To check tokens on the backend, log in with the appropriate token. Tokens can be obtained using the /user/login/ endpoint

/user/me waiting for an access token to enter

/user/me/jwt/refresh_access_token waiting for a refresh token to enter